I think you're seeing what you want to see. To begin with Ian is hardly just interested in Alison. Even if he says he likes her, he's also effectively telling everybody else, how much more he likes Lena. So it's not surprising, that Alison and Jeremy as well for that matter, is getting mixed messages from Ian about what he really wants. That's why Alison is willing to have sex with Jeremy, even if she only really wants Ian. Ian tells Jeremy on several occasions, how much he fancies Lena as well, which would suggest to someone like Jeremy, that he's not interested in being exclusive with Alison. So why wouldn't he take the opportunity to have sex with her, if Alison wants it as well?
In the early part of the game, Alison is always second best in Ian's mind. He's pretty much only thinking about Lena. And until he decides, him and her are not going to be an item after all, or he can have fun with more than one girl at the same time, Ian is pretty confused about how he really feels towards Alison. Which is why everyone keeps asking him about Lena and insinuating that him and her are a 'thing'.
